scholarly journals Dynamic Allostery Highlights the Evolutionary Differences between the CoV-1 and CoV-2 Main Proteases

2021 ◽  
Author(s):  
P. Campitelli ◽  
J. Lu ◽  
S. B. Ozkan
Keyword(s):  
Comparative Analysis ◽  
Active Sites ◽  
Distal Region ◽  
Catalytic Site ◽  
Dynamic Coupling ◽  
Long Distance ◽  
Inhibitor Binding ◽  
Coupling Index ◽  
Two Systems ◽  
Biophysical Changes

ABSTRACTThe SARS-CoV-2 coronavirus has become one of the most immediate and widely-studied systems since its identification and subsequent global outbreak from 2019-2020. In an effort to understand the biophysical changes as a result of mutations, the mechanics of multiple different proteins within the SARS-CoV-2 virus have been studied and compared with SARS-CoV-1. Focusing on the main protease (mPro), we first explored the long range dynamic-relationship, particularly in cross-chain dynamics, using the Dynamic Coupling Index (DCI) to investigate the dynamic coupling between the catalytic site residues and the rest of the protein, both inter and intra chain for the CoV-1 and CoV-2 mPro. We found that there is significant cross-chain coupling between these active sites and distal residues in the CoV-2 mPro but it was missing in CoV-1. The enhanced long distance interactions, particularly between the two chains, suggest subsequently enhanced cooperativity for CoV-2. A further comparative analysis of the dynamic flexibility using the Dynamic Flexibility Index (DFI) between the CoV-1 and CoV-2 mPros shows that the inhibitor binding near active sites induces change in flexibility to a distal region of the protein, opposite in behavior between the two systems; this region becomes more flexible upon inhibitor binding in CoV-1 while it becomes less flexible in the CoV-2 mPro. Upon inspection, we show that, on average, the dynamic flexibility of the sites substituted from CoV-1 to CoV-2 changes significantly less than the average calculated across all residues within the structure, indicating that the differences in behaviors between the two systems is likely the result of allosteric influence, where the new substitutions in COV-2 induce flexibility and dynamical changes elsewhere in the structure.SIGNIFICANCEHere we have conducted a comparative analysis between the SARS-CoV-1 and SARS-CoV-2 mPro systems to shed mechanistic insight on the biophysical changes associated with the mutations between these two enzymes. Our work shows that the CoV-2 mPro system exhibits enhanced cross-chain communication between catalytic site residues and the rest of the structure. Further, both dynamic coupling and dynamic flexibility analyses indicates that, largely, the dynamic changes as evaluated by DCI and DFI occur at sites other than the mutation sites themselves, indicating that the functional differences between these two proteins are a result of dynamic allostery

scholarly journals Mutations Utilize Dynamic Allostery to Confer Resistance in TEM-1 β-lactamase

2018 ◽  
Vol 19 (12) ◽  
pp. 3808 ◽  
Author(s):  
Tushar Modi ◽  
S. Ozkan
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Critical Role ◽  
Conformational Dynamics ◽  
Driver Mutations ◽  
Common Mechanism ◽  
Dynamic Coupling ◽  
Long Distance ◽  
Coupling Index ◽  
High Dynamic

β-lactamases are enzymes produced by bacteria to hydrolyze β-lactam antibiotics as a common mechanism of resistance. Evolution in such enzymes has been rendering a wide variety of antibiotics impotent, therefore posing a major threat. Clinical and in vitro studies of evolution in TEM-1 β-lactamase have revealed a large number of single point mutations that are responsible for driving resistance to antibiotics and/or inhibitors. The distal locations of these mutations from the active sites suggest that these allosterically modulate the antibiotic resistance. We investigated the effects of resistance driver mutations on the conformational dynamics of the enzyme to provide insights about the mechanism of their long-distance interactions. Through all-atom molecular dynamics (MD) simulations, we obtained the dynamic flexibility profiles of the variants and compared those with that of the wild type TEM-1. While the mutational sites in the variants did not have any direct van der Waals interactions with the active site position S70 and E166, we observed a change in the flexibility of these sites, which play a very critical role in hydrolysis. Such long distance dynamic interactions were further confirmed by dynamic coupling index (DCI) analysis as the sites involved in resistance driving mutations exhibited high dynamic coupling with the active sites. A more exhaustive dynamic analysis, using a selection pressure for ampicillin and cefotaxime resistance on all possible types of substitutions in the amino acid sequence of TEM-1, further demonstrated the observed mechanism. Mutational positions that play a crucial role for the emergence of resistance to new antibiotics exhibited high dynamic coupling with the active site irrespective of their locations. These dynamically coupled positions were neither particularly rigid nor particularly flexible, making them more evolvable positions. Nature utilizes these sites to modulate the dynamics of the catalytic sites instead of mutating the highly rigid positions around the catalytic site.

scholarly journals Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants

2021 ◽  
Author(s):  
Nicholas James Ose ◽  
Brandon M. Butler ◽  
Avishek Kumar ◽  
Maxwell Sanderford ◽  
Sudhir Kumar ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Conformational Dynamics ◽  
Mechanistic Explanation ◽  
Missense Mutations ◽  
Active Site Residues ◽  
Dynamic Coupling ◽  
Long Distance ◽  
Functional Sites ◽  
Missense Variants

Many pathogenic missense mutations are found in protein positions that are neither well-conserved nor belong to any known functional domains. Consequently, we lack any mechanistic underpinning of dysfunction caused by such mutations. We explored the disruption of allosteric dynamic coupling between these positions and the known functional sites as a possible mechanism for such mutations. In this study, we present an analysis of 144 human enzymes containing 591 pathogenic missense variants, in which allosteric dynamic coupling of mutated positions with known active sites provides insights into a primary biophysical mechanism and evidence of their functional importance. We illustrate this mechanism in a case study of β-Glucocerebrosidase (GCase), which contains 94 Gaucher disease-associated missense variants located some distance away from the active site. An analysis of the conformational dynamics of GCase suggests that mutations on these distal sites cause changes in the flexibility of active site residues despite their distance, indicating a dynamic communication network throughout the protein. The disruption of the long-distance dynamic coupling due to the presence of missense mutations may provide a plausible general mechanistic explanation for biological dysfunction and disease.

scholarly journals Insight into Inhibitor Binding in the Eukaryotic Proteasome: Computations of the 20S CP

2018 ◽  
Vol 19 (12) ◽  
pp. 3858
Author(s):  
Milan Hodošček ◽  
Nadia Elghobashi-Meinhardt
Keyword(s):  
Electrostatic Interactions ◽  
Active Sites ◽  
Sampling Period ◽  
Md Simulations ◽  
Structural Features ◽  
Relaxation Dynamics ◽  
Inhibitor Binding ◽  
Computational Analyses ◽  
Insight Into ◽  
Proteolytic Chamber

A combination of molecular dynamics (MD) simulations and computational analyses uncovers structural features that may influence substrate passage and exposure to the active sites within the proteolytic chamber of the 20S proteasome core particle (CP). MD simulations of the CP reveal relaxation dynamics in which the CP slowly contracts over the 54 ns sampling period. MD simulations of the SyringolinA (SylA) inhibitor within the proteolytic B 1 ring chamber of the CP indicate that favorable van der Waals and electrostatic interactions account for the predominant association of the inhibitor with the walls of the proteolytic chamber. The time scale required for the inhibitor to travel from the center of the proteolytic chamber to the chamber wall is on the order of 4 ns, accompanied by an average energetic stabilization of approximately −20 kcal/mol.

scholarly journals On Harmonization of Business Accounting and the SNA

2020 ◽  
Vol 27 (5) ◽  
pp. 16-22
Author(s):  
Yu. N. Ivanov ◽  
T. A. Khomenko
Keyword(s):  
Comparative Analysis ◽  
National Accounts ◽  
Information Base ◽  
Wide Range ◽  
Analytical Work ◽  
Two Systems ◽  
The Usa ◽  
The Russian Federation ◽  
Ministry Of Finance

The article considers a wide range of questions pertaining to possible and applicable harmonization of business accounting and the SNA which would, if implemented, facilitate the improvement of the information base for the compilation of national accounts and consistency of analysis of economy at micro and macro levels. The authors note that total harmonization of the two systems of information cannot be achieved due to diff erences in their key objectives. The harmonization of selected indicators and classifi cation, however, is possible and useful. In this context, the views on this matter of internationally-recognized national accounts experts, such as R. Ruggles (the USA) and F. Bos (the Netherlands), are commented on. A comparative analysis of concepts and defi nitions of some indicators of both systems is presented in the article. In particular, the diff erences between the income defi nitions. For instance, it is noted that the SNA defi nition of income is based on the concept developed by J. Hiсks and it excludes income from sales of assets and holding gains, whereas in business accounting this method is not adopted. The diff erences between two systems in defi nitions of sale of output, input, profi t and methods of valuation of indicators are also described in the article. The authors substantiate the possible directions and sequence of individual steps to the harmonization of the SNA and business accounting in the Russian Federation. They emphasize the need for close interaction between Rosstat and the Ministry of Finance of Russia in carrying out this vital work, which is necessary for creating single information, statistical and methodological space in Russia, to improve the quality of statistics and accounting, analytical work in general and management decisions.

The Nature and Use of Unilateral Executive Measures

2021 ◽  
pp. 137-164
Author(s):  
Margit Cohn
Keyword(s):  
Comparative Analysis ◽  
Legal Status ◽  
Extensive Study ◽  
The State ◽  
Executive Orders ◽  
Strong Similarity ◽  
Unilateral Action ◽  
Comparative Methodology ◽  
Two Systems ◽  
Structural Regime

Constitutions and constitutional constructs offer executives a repository of fuzzy sources of power which enable unilateral action. This chapter focuses on one of these forms: executive making of (semi)-formal unilateral measures. These orders and edicts have an important edge: on their face, they are ‘lawlike’, and seemingly carry the imprimatur of binding law, even when their legal status is fuzzy. The chapter uses comparative methodology in order to show the strong similarity between such measures as they emerged and continue to be applied in the two systems compared in this book. Orders in Council, Executive Orders and the like, such as the ones brought before the courts in Bancoult and Youngstown, have been at the focus of extensive study; yet to date, such measures, issued in both systems, have never been conjointly discussed. This chapter offers the first comparative analysis. This novel comparative exercise leads to the discovery of a surprising convergence—surprising, if attention is focused on structural regime elements. The findings support two of the main themes advanced in this book: that the emergence and retention of fuzzy legality is an unavoidable feature of the state, despite the ingrained danger it poses to the proper functioning of democracies. A third theme, concerned with the need to constrain fuzziness by robust judicial oversight, is addressed in the last chapter of this book. This chapter also offers new insights on the unclear distinction between constitutional- and statute-derived fuzziness, again, a feature shared by both systems.

scholarly journals Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation

2020 ◽  
Vol 6 (14) ◽  
pp. eaay7919
Author(s):  
Nandini Sharma ◽  
Navjeet Ahalawat ◽  
Padmani Sandhu ◽  
Erick Strauss ◽  
Jagannath Mondal ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Active Sites ◽  
Long Distance ◽  
Dynamic Interactions ◽  
Interface Control ◽  
Protein Energy ◽  
Catalytic Loop ◽  
Ammonia Tunnel ◽  
Dynamics Simulations

Transient tunnels that assemble and disassemble to facilitate passage of unstable intermediates in enzymes containing multiple reaction centers are controlled by allosteric cues. Using the 140-kDa purine biosynthetic enzyme PurL as a model system and a combination of biochemical and x-ray crystallographic studies, we show that long-distance communication between ~25-Å distal active sites is initiated by an allosteric switch, residing in a conserved catalytic loop, adjacent to the synthetase active site. Further, combinatory experiments seeded from molecular dynamics simulations help to delineate transient states that bring out the central role of nonfunctional adaptor domains. We show that carefully orchestrated conformational changes, facilitated by interplay of dynamic interactions at the allosteric switch and adaptor-domain interface, control reactivity and concomitant formation of the ammonia tunnel. This study asserts that substrate channeling is modulated by allosteric hotspots that alter protein energy landscape, thereby allowing the protein to adopt transient conformations paramount to function.

scholarly journals Substitutions at Nonconserved Rheostat Positions Modulate Function by Rewiring Long-Range, Dynamic Interactions

2020 ◽  
Vol 38 (1) ◽  
pp. 201-214 ◽  
Author(s):  
Paul Campitelli ◽  
Liskin Swint-Kruse ◽  
S Banu Ozkan
Keyword(s):  
Dna Binding ◽  
Long Range ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Dynamic Coupling ◽  
Long Distance ◽  
Repressor Protein ◽  
Functional Changes ◽  
Lactose Repressor ◽  
Wide Range

Abstract Amino acid substitutions at nonconserved protein positions can have noncanonical and “long-distance” outcomes on protein function. Such outcomes might arise from changes in the internal protein communication network, which is often accompanied by changes in structural flexibility. To test this, we calculated flexibilities and dynamic coupling for positions in the linker region of the lactose repressor protein. This region contains nonconserved positions for which substitutions alter DNA-binding affinity. We first chose to study 11 substitutions at position 52. In computations, substitutions showed long-range effects on flexibilities of DNA-binding positions, and the degree of flexibility change correlated with experimentally measured changes in DNA binding. Substitutions also altered dynamic coupling to DNA-binding positions in a manner that captured other experimentally determined functional changes. Next, we broadened calculations to consider the dynamic coupling between 17 linker positions and the DNA-binding domain. Experimentally, these linker positions exhibited a wide range of substitution outcomes: Four conserved positions tolerated hardly any substitutions (“toggle”), ten nonconserved positions showed progressive changes from a range of substitutions (“rheostat”), and three nonconserved positions tolerated almost all substitutions (“neutral”). In computations with wild-type lactose repressor protein, the dynamic couplings between the DNA-binding domain and these linker positions showed varied degrees of asymmetry that correlated with the observed toggle/rheostat/neutral substitution outcomes. Thus, we propose that long-range and noncanonical substitutions outcomes at nonconserved positions arise from rewiring long-range communication among functionally important positions. Such calculations might enable predictions for substitution outcomes at a range of nonconserved positions.

On Lorenz and Chen Systems

2018 ◽  
Vol 28 (01) ◽  
pp. 1850018 ◽  
Author(s):  
Ruy Barboza
Keyword(s):  
Comparative Analysis ◽  
Two Systems

In this work, a simple comparative analysis on the Lorenz and the Chen systems is presented, in order to understand some aspects that make these two systems distinct from one another.

Investigation of the Catalytic Properties of the Dysthrombin, Thrombin Quick

1979 ◽  
Author(s):  
R.A. Henriksen ◽  
W.G. Owen ◽  
M.E. Nesheim ◽  
K.G. Mann
Keyword(s):  
Active Site ◽  
Mayo Clinic ◽  
Active Sites ◽  
Fluorescence Enhancement ◽  
Catalytic Mechanism ◽  
Antithrombin Iii ◽  
Catalytic Properties ◽  
Inhibitor Binding ◽  
Equivalent Number ◽  
Aggregation Of Platelets

Thrombin Quick (TQ) may be isolated following treatment of Prothrombin Quick [Owen, et al, Mayo Clinic Proceedings, 53: 29-33, (1978)] with Taipan venom, phospholipid and Ca2+. The clotting activity of TQ with fibrinogen is 1/200 that of normal thrombin (T) The activation of Factors V and VIII, and the aggregation of platelets by TQ occurs with an effectiveness of about 1/50 that of thrombin. When incubated with antithrombin III, both T and TQ form inhibitor complexes as determined by dodecylsulfate gel electropheresis. Titration of T and TQ with the fluorescent inhibitor dansylarginine-4-ethylpiperidine amide indicates an equivalent number of active sites based on protein absorption at 280 nm. However, the two enzymes may be distinguished by the decreased fluorescence enhancement observed with TQ relative to T, indicating an increased polarity in the inhibitor binding site of TQ. With the substrate benzoylarginine ethylester, TQ has a Km = 4.5 x 10-5M and kcat - 6.93 compared to Km = 4.0 × 10-5M and kcat = 17.7 for T. This indicates that the defect in TQ esterase activity is in the catalytic mechanism itself and not in substrate binding. The rate of inhibition of TQ by diisopropylphosphofluoridate is decreased. Decreased acylation and deacylation rates for TQ relative to T are observed for tydrolysis of the active site titrant 4-methyumbel1 i feryl-p-guanidlnobenzoate.

scholarly journals Research and development of commercial lidar systems in romania: critical review of the ESYRO lidar systems developed by sc enviroscopy SRL (ESYRO)

2018 ◽  
Vol 176 ◽  
pp. 11005 ◽  
Author(s):  
Marius Mihai Cazacu ◽  
Ovidiu Tudose ◽  
Dragos Balanici ◽  
Ioan Balin
Keyword(s):  
Comparative Analysis ◽  
Research And Development ◽  
Critical Review ◽  
Saharan Dust ◽  
Lidar System ◽  
Two Systems ◽  
Multi Wavelength ◽  
System Configurations

This paper is shortly presenting the two basic lidar system configurations respectively a micro-lidar and a multi-wavelength lidar systems developed by SC EnviroScopY SRL (ESYRO) from Iasi – Romania in the last decade. Furthermore in addition to the comparative analysis of the two technical configurations the examples of various tests and the capability of the two systems to perform are here presented. Measurements samples of aerosols, clouds, PBL, depolarization and Saharan dust are also illustrated.

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